Journal Article

WGCNA and transcriptome profiling reveal hub genes for key development stage seed size/oil content between wild and cultivated soybean

Xiong, Erhui, Quan, Leipo, Zhu, Xuling, Lu, Weiguo, Li, Ke, Lu, Wenyan, Zhou, Xinan, Zhang, Dan, Lian, Yun, Chen, Xiaoming, Jiao, Yongqing, Chu, Shanshan, Li, Junfeng, Qu, Xuelian, Liu, Hongli, Yao, Yanjie, Chen, Meiling

2023

Overview

Background Soybean is one of the most important oil crops in the world. The domestication of wild soybean has resulted in significant changes in the seed oil content and seed size of cultivated soybeans. To better understand the molecular mechanisms of seed formation and oil content accumulation, WDD01514 (E1), ZYD00463 (E2), and two extreme progenies (E23 and E171) derived from RILs were used for weighted gene coexpression network analysis (WGCNA) combined with transcriptome analysis. Results In this study, both seed weight and oil content in E1 and E171 were significantly higher than those in E2 and E23, and 20 DAF and 30 DAF may be key stages of soybean seed oil content accumulation and weight increase. Pathways such as “Photosynthesis”, “Carbon metabolism”, and “Fatty acid metabolism”, were involved in oil content accumulation and grain formation between wild and cultivated soybeans at 20 and 30 DAF according to RNA-seq analysis. A total of 121 oil content accumulation and 189 seed formation candidate genes were screened from differentially expressed genes. WGCNA identified six modules related to seed oil content and seed weight, and 76 candidate genes were screened from modules and network. Among them, 16 genes were used for qRT-PCR and tissue specific expression pattern analysis, and their expression-levels in 33-wild and 23-cultivated soybean varieties were subjected to correlation analysis; some key genes were verified as likely to be involved in oil content accumulation and grain formation. Conclusions Overall, these results contribute to an understanding of seed lipid metabolism and seed size during seed development, and identify potential functional genes for improving soybean yield and seed oil quantity.

• Publisher: BioMed Central,BioMed Central Ltd,Springer Nature B.V,BMC
• Subject: Accumulation / Agricultural research / Analysis / Animal Genetics and Genomics / Applications software / Biomedical and Life Sciences / Biosynthesis / Computational biology / Correlation analysis / Crop yield / Crop yields / Cultivation / Developmental stages / Domestication / Edible Grain / Fabaceae / Fatty acids / Gene expression / Gene Expression Profiling / Genes / Genetic aspects / Genetic research / Genomics / Glycine max - genetics / Life Sciences / Lipid metabolism / Lipids / Metabolism / Microarrays / Microbial Genetics and Genomics / Modules / Molecular modelling / Network analysis / Oil content / Oils & fats / Oilseeds / Pattern analysis / Photosynthesis / Physiological aspects / Plant Genetics and Genomics / Plant Oils / Production processes / Proteomics / RNA sequencing / Seed size / Seeds / Seeds - genetics / Soy oil / Soybean / Soybeans / Synthesis / Transcriptome / Transcriptomes / Vegetable oils / Weight / WGCNA